Running ANGSD using multiple -doMaf options at once

Question

[ggman]

Hello friends,

I am attempting to obtain a csv file running angsd with the following data

chromo   position   major   minor   ref   knownEM   unknownEM   nInd

When I run angsd using the command below, it appears to be ignoring -doMaf 2 and only outputting my results as if it only ran -doMaf 1 which appears to not be the case as the run is taking significantly longer to run if I only ran it with -doMaf 1 as opposed to -doMaf 1,2. I would appreciate any suggestions on how to obtain both knownEM and unknownEM through angsd. My last resort is running both separately and merging the results with a little bit of coding.

angsd -out out -doMajorMinor 2 -doMaf 1,2 -sbamlist.txt -doCounts 1 -GL 1 -P 150

Current Output

chromo   position   major   minor   ref   knownEM   nInd

Expected Output

chromo   position   major   minor   ref   knownEM   unknownEM   nInd

Answer 1

[andersdetermig]

you should add the numbers together "-domaf 3" ( 1+2´=3 )